Clay minerals and the origin of life



T

Tim Tyler

Guest
I wrote an essay recently expressing some of my frustration at the "sluggish" response of other
scientists to Cairns-Smith's clay theory of life's origin.

One of the reasons I think it is important to get the origin theory straight is due to the fact that
a good theory of how life formed on the planet naturally seems likely to be one of the best
foundations on which to rest attempts to recreate the abiogenesis event.

The essay below is reprinted from: http://originoflife.net/neglect/

Other material about the theory: http://originoflife.net/

...including many references: http://originoflife.net/cairns_smith/

The neglect of the clay theory
==============================

Neglect
-------
Since is is pretty clear that clay minerals form by far the most likely basis for the earliest
living systems, historians of science will no-doubt be curious to learn how the theory associated
with this idea came to be neglected for some 37 years after it was first explained - despite the
eloquent elucidation of the theory - and the lack of any serious objections to it.

Reasons
-------
Here's my take on the matter:

1. The theory is not obvious or intuitive - and the originator of the theory - A. G. Cairns-Smith
himself found it appropriate to explain its discovery using the metaphor of detective work;

2. The theory suggests that a whole new bunch of genetic materials were involved - surely Occam's
razor would suggest that the first organisms are not so different from the modern ones;

3. The idea of a genetic takeover can seems far-fetched and unnecessary, and we have no clear
example of the process ever occurring;

4. There is a lot of systematic evidence that seems to point towards carbon chemistry
being involved.

Explanation
-----------
I'm inclined to think that the last point is the telling one:

Humans sponsor a lot of research into organic chemistry and nucleic acids - since they are
themselves constructed out of organic chemistry and nucleic acids. Every once in a while this
produces results that may be relevant in some way to life's origin.

Of course this research is valuable - but it creates a continuous association between the question
of life's origin and organic chemistry - so that those interested in life's origin tend to get drawn
into organic chemistry - and it is organic chemists who get their research in this area funded.

This association is a self-perpetuating one - the more research is done in the area the more
discoveries will be made suggesting that RNA, PNA - or whatever - is involved in the origin of life.

Little or no evidence is likely to be found by a similar approach for the clay theory - since the
clays were most probably long gone before RNA came onto the scene - and it isn't reasonable to
expect to find many scars of such an ancient and archaic genetic material in modern organisms.

The situation is like that of the drunk searching for his key:

A man watched a drunk searching for something on the ground. "What have you lost?" he asked.

"My key," said the drunk.

So the man when down on his knees too, and they both looked for it. After a time, the other man
asked, "Where exactly did you drop it?"

"Up the road a bit," the drunk replied.

"Then why aren't you looking for it there?"

The drunk gives him a confused look. "'Cause there's more light here than up the road."

Just as the drunk looks for his key where there is the most light - so the origin researcher will be
drawn to where there are the most published studies.

Unfortunately in this case, this will lead them well away from the truth.

Worse, the more studies there are that relate to the link between carbon chemistry and the origin of
life, the more the association will sink into people's unconsciousness, and the harder it will be to
get funding to explore other theories.

Significance
------------
I'm sure eventually the best theory will win out.

No doubt, researchers into the organic origin of life will eventually be seen to be like a large
group of people standing around looking up - each straining to see what all the others are
looking at.

However, that is certainly not the current situation - and I hate seeing such obviously-incorrect
theories in dominant positions.

It seems especially important to topple the notion of an organic origin to life quickly - since
theories of the origin of life have a dramatic impact on the sort of experiments which are done
in attempting to replicate the abiogenesis event - and the attempt to create living physical
systems from scratch may form an important part of mankind's exploration of nanotechnology in the
coming century.

Prospects
---------
Outside Cairns-Smith's work there has been little published about the technical aspects of his
theory. Those interested in clay minerals as industrial catalysts simply have not known about or
been interested in the origin of life.

Fortunately - as evidence for the intimate association between clay minerals and the origin of life
(due to their properties as catalysts) grows - this seems likely to change
- at least a little.

Perhaps this phenomenon will lead to some increased interest in Cairns-Smith's theories again.

Will people look again at some electron micrographs, see that there is a lot more high-fidelity
information copying going on there than has ever been shown with any plausible prebiotic organic
compounds - and reexamine the theory?

I certainly hope so - an intelligent review is now long overdue - and it is frustrating waiting
around for other scientists to catch on.

- http://originoflife.net/neglect/
--
__________
|im |yler http://timtyler.org/ [email protected] Remove lock to reply.
 
Tim Tyler writes
> I wrote an essay recently expressing some of my frustration at the "sluggish" response of other
> scientists to Cairns-Smith's clay theory of life's origin. [snip] Since is is pretty clear that
> clay minerals form by far the most likely basis for the earliest living systems, historians of
> science will no-doubt be curious to learn how the theory associated with this idea came to be
> neglected for some 37 years after it was first explained - despite the eloquent elucidation of the
> theory - and the lack of any serious objections to it.

I disagree that Cairns-Smith's work has been neglected. His idea of genetic takeover, and his
metaphor of the arch are enormously influential. Same goes for his pointing out the relevance of
surface chemistry to people who only understand solution chemistry.

Yes, the specific idea of clay is out of favor now, and, personally I believe that there are good
reasons for this, but even if pyrite replaces clay as the magic mineral of choice, historians will
still point to Cairns-Smith's ideas as pivotal.

Tyler expects too much of a sluggish establishment. How many years did it take before Oparin's ideas
became mainsteam?

Tyler goes on to complain about how the association between life and carbon results in a vicious
cycle of reasearch funding:

> This association is a self-perpetuating one - the more research is done in the area the more
> discoveries will be made suggesting that RNA, PNA - or whatever - is involved in the origin
> of life.
>
> Little or no evidence is likely to be found by a similar approach for the clay theory - since the
> clays were most probably long gone before RNA came onto the scene - and it isn't reasonable to
> expect to find many scars of such an ancient and archaic genetic material in modern organisms.
> [snip] Worse, the more studies there are that relate to the link between carbon chemistry and the
> origin of life, the more the association will sink into people's unconsciousness, and the harder
> it will be to get funding to explore other theories.

But, if clay has left no clues behind, what exactly is it that clay researchers will do if they do
get funding?

But that is enough criticism of Tyler, who has written a very nice post here.

I am curious, though as to why it is not reasonable to expect to find scars after a genetic
takeover. There are people who claim to see scars of an RNA/ribozyme genetics in our current DNA/protein-
enzyme genetic system. In my own theorizing about pre-RNA genetic mechanisms I expect (and fondly
hope) to find scars. Why should we not expect clay to have left scars?

I am also curious as to why you write "the clays were most probably long gone before RNA came onto
the scene". You seem to assume that there were many genetic takeovers. Your lamp-post/key parable
notwithstanding, doesn't if make sense to research the most recent takeovers first, since they are
the ones that presumably left the most evidence?

PS. I haven't read your posted papers yet. I look forward to doing so.
 
<< Here's my take on the matter:

1. The theory is not obvious or intuitive - and the originator of the theory - A. G. Cairns-Smith
himself found it appropriate to explain its discovery using the metaphor of detective work;

2. The theory suggests that a whole new bunch of genetic materials were involved - surely Occam's
razor would suggest that the first organisms are not so different from the modern ones;

3. The idea of a genetic takeover can seems far-fetched and unnecessary, and we have no clear
example of the process ever occurring;

4. There is a lot of systematic evidence that seems to point towards carbon chemistry
being involved.

TH I think that clay was a part of the process, an important catalyst but the whole ball of wax?
With that in mind I'll ask two questions.

5. Can you outline a complete scenario from clay to the point where there is metabolism, replcation,
and a dividing cell - maybe even an RNA world.
6. What environmental conditions is all this happening in? And how does the daily sun heat cycle,
and the seasonal change on earth effect this scenario?

Tom Hendricks
 
"Tim Tyler" <[email protected]> wrote in message
news:[email protected]...
> Jim Menegay <[email protected]> wrote or quoted:
> > Tim Tyler <[email protected]> wrote in message
news:<[email protected]>...
>
[snippage]

> > We can easily imagine "genetic takeovers".
> >
> > But only a few people worry that "organismic takeovers"
might be more
> > difficult to pull off. How do you gradually evolve a
membrane? [...]
>
> Barriers that hold things together can be built on many
scales - from
> cell walls to sea shells and insect exoskeletons - so they
have
> evolved on multiple occasions.
>
> The original evolution of cell membranes is hypothesised
to have ocurred
> on mineral surfaces - with a lipid layer initially binding
loosely to
> the surface, and then forming blisters and eventually
cells.
>
> The gap between the mineral surface and the lipid layer
provides
> nutrients and exhaust routes - since expecting very much
to make
> it through a primitive membrane is not very resonable.
>
> See, "The Origins of Life" - JMS & ES, p. 56 for a
diagram.

It's so tempting to presume a purely simplistic reductionist viewpoint and contemplate life's
evolution being the iterative merging of two smaller units to form a larger/more complex one--genes
(or proto-genes) absorbed on a substrate to form a primitive chromosome, the latter absorbed

solution or suspension, spherical bi-layer droplet) ... evolution of primitive prokaryote which then
absorbs another, forming the nucleus for a eukaryote, and the building blocks evolve into complex
organisms. The only question is where do genes come from?--Are there any good models outside of Kaufman-
like autocatylytic enzyme chains in a non-linear dynamic "soup" far from equilibrium...chaos...and
chance? ...tonyC
> --
> __________
> |im |yler http://timtyler.org/ [email protected] Remove
lock to reply.
 
"Jim Menegay" <[email protected]> wrote in message
news:[email protected]...
> Anthony Cerrato <[email protected]> wrote in message
news:<[email protected]>...
> > ... [Snip] ...The only question is where do genes come from?--Are there any
good
> > models outside of Kaufman-like autocatylytic enzyme
chains
> > in a non-linear dynamic "soup" far from equilibrium...chaos...and chance? ...tonyC
>
> It is odd, to say the least, to respond twice to the same
question,
> especially when the question was not directed to me. ;-/
But it
> occurs to me, on reflection, that my first answer may have
completely
> missed your point.
>
> Are you suggesting that some other process (besides
natural selection)
> is needed in order to somehow "bootstrap" a collection of
random
> genes into a collection of somewhat effective genes? And,
that
> natural selection cannot, somehow, "gain traction" until
this takes
> place? That only a somewhat-effective starter system can
evolve to
> a very-effective final system under natural selection?

No, I wasn't suggesting anything like that--interesting question though. I don't really think that
anything besides neo-Darwinian evolution is required, once just a relatively chemically stable proto-
gene is originated.

> I suspect that Tim would deny that any such bootstrap
process is needed.
> Me, I'm intrigued by the suggestion, but dubious that
Kauffman is
> on the right track regarding the nature of the bootstrap,
if one is
> actually needed.

I think the only thing needed as the initial bootstrap to life itself is the general autocatylitic
processes/conditions Kauffman describes--with the right mix of _myriad_ autocatylitic polymers and
enzymes (for activation energy lowering) that IS the bootstrap, isn't it?
:) I don't recall his mention of specific bootstrapping
otherwise though in this context in his book, At Home in the Universe: The Search for Laws of Self-
Organization and Complexity (which is all of his I've read--and that was a while ago.) ...tonyC
 
"Tim Tyler" <[email protected]> wrote in message
news:[email protected]...
> Jim Menegay <[email protected]> wrote or quoted:
> > Anthony Cerrato <[email protected]> wrote:
>
> >> The only question is where do genes come from?--Are
there any good
> >> models outside of Kaufman-like autocatylytic enzyme
chains in a
> >> non-linear dynamic "soup" far from
equilibrium...chaos...and chance?
>
> [...]
>
> > Are you suggesting that some other process (besides
natural selection)
> > is needed in order to somehow "bootstrap" a collection
of random
> > genes into a collection of somewhat effective genes?
And, that
> > natural selection cannot, somehow, "gain traction" until
this takes
> > place? That only a somewhat-effective starter system
can evolve to
> > a very-effective final system under natural selection?
> >
> > I suspect that Tim would deny that any such bootstrap
process is needed.
> > Me, I'm intrigued by the suggestion, but dubious that
Kauffman is
> > on the right track regarding the nature of the
bootstrap, if one is
> > actually needed.
>
> I usually take "genes" to refer to the heritable bits of a
model -
> rather than to some specific physical entity - so "before
genes"
> there can have been no natural selection going on.

Yes, that is reasonable and I would too. Funny though, that with all we know now about biotech
today, it is still often so difficult to refer to the simplest unit of heredity without qualifying
the specific definition--but I guess that's inevitable due to the physicochemical rather than
biological historical development pathway taken to get to the DNA model.

> What /did/ exist before evoultion started was ordinary
physics and
> chemistry. There is substantial scope for these
exhibiting complex
> phenomena - from processes usually described using the
term
> "self-organisation".
>
> Plainly my preferred explanation invokes such
self-organisation,
> prior to the origin of self-reproduction.
>
> Crystal growth is a classic example of highly ordered
structures
> forming out of a disordered molecular soup.

And everything that happened after the birth of any first speck of organized replicating life is easy--
just say Darwin! :) ...tonyC

> --
> __________
> |im |yler http://timtyler.org/ [email protected] Remove
lock to reply.
 
Jim Menegay <[email protected]> wrote or quoted:
> Tim Tyler writes

>> I wrote an essay recently expressing some of my frustration at the "sluggish" response of other
>> scientists to Cairns-Smith's clay theory of life's origin. [snip] Since is is pretty clear that
>> clay minerals form by far the most likely basis for the earliest living systems, historians of
>> science will no-doubt be curious to learn how the theory associated with this idea came to be
>> neglected for some 37 years after it was first explained - despite the eloquent elucidation of
>> the theory - and the lack of any serious objections to it.
>
> I disagree that Cairns-Smith's work has been neglected. His idea of genetic takeover, and his
> metaphor of the arch are enormously influential. Same goes for his pointing out the relevance of
> surface chemistry to people who only understand solution chemistry.

There's some truth to this. While fairly widely recognised I still think the idea of genetic
takeovers needs to sink in a bit more.

I guess it's the clay genes I was primarily referring to.

> Tyler goes on to complain about how the association between life and carbon results in a vicious
> cycle of reasearch funding:
>
>> This association is a self-perpetuating one - the more research is done in the area the more
>> discoveries will be made suggesting that RNA, PNA - or whatever - is involved in the origin
>> of life.
>>
>> Little or no evidence is likely to be found by a similar approach for the clay theory - since the
>> clays were most probably long gone before RNA came onto the scene - and it isn't reasonable to
>> expect to find many scars of such an ancient and archaic genetic material in modern organisms.
>> [snip] Worse, the more studies there are that relate to the link between carbon chemistry and the
>> origin of life, the more the association will sink into people's unconsciousness, and the harder
>> it will be to get funding to explore other theories.
>
> But, if clay has left no clues behind, what exactly is it that clay researchers will do if they do
> get funding?

There are other approaches to exploring life's origins besides looking for scars in modern
orgainsms.

The clay theory suggests that a number of clay minerals may represent low level life - and exhibit
adaptations to their environments.

Basically the other approaches mostly involve either looking for existing clay organisms in their
natural environment - or trying to *create* clay organisms.

If creating organisms from clay proves much easier than other approaches to synthesizing life, then
the clay theory becomes more likely.

> I am curious, though as to why it is not reasonable to expect to find scars after a genetic
> takeover. There are people who claim to see scars of an RNA/ribozyme genetics in our current DNA/protein-
> enzyme genetic system. In my own theorizing about pre-RNA genetic mechanisms I expect (and fondly
> hope) to find scars. Why should we not expect clay to have left scars?

RNA -> DNA probably was probably not a genetic takover - rather the old messages were read by the
new machinery.

Genetic takeovers are likely to leave systematically fewer traces than modifications of the genetic
material - since they have the luxury of starting more-or-less from scratch.

The first nucleic acid likely played a structural role before it played a genetic one - and it might
be possible to find signs of that.

However the clay is most likely long gone. Later genetic materials were not derived directly from it
- but rather from the products of reactions it catalysed. There's a lot of scope in such a
relationship for kicking over traces - and after what may have been several such takeovers, it is
expecting a lot to find much trace of the earliest organisms in those that remain today.

It's rather like opening up a TV and expecting to find traces of a printing press inside - the old
technology is nowhere to be found; it has been discarded.

> I am also curious as to why you write "the clays were most probably long gone before RNA came onto
> the scene". You seem to assume that there were many genetic takeovers.

I don't have a very clear idea of how many genetic takeovers there have been so far. There may have
been quite a long string of them - or it may have been just one or two.

Nor do I know how many there are yet to come - it may be just one or two - or again, there may be
quite a long string of them.

> Your lamp-post/key parable notwithstanding, doesn't if make sense to research the most recent
> takeovers first, since they are the ones that presumably left the most evidence?

Working backwards is fine and important work. However, I think it is unlikely to take researchers
back as far as life's origin.

For that, I think another approach is needed - survey the possible ways in which life /might/ have
formed - and experimentally investigate their probabilities of success.
--
__________
|im |yler http://timtyler.org/ [email protected] Remove lock to reply.
 
Jim Menegay <[email protected]> wrote or quoted:

> I disagree that Cairns-Smith's work has been neglected. His idea of genetic takeover, and his
> metaphor of the arch are enormously influential. [...]

Perhaps a good example of the failure of genetic takeovers to influence the thinking of biologists
lies in observing that they don't get so much as a mention in J. Maynard Smith's "The Major
Transitions of Evolution".

Personally, I can't think of much more of a "major transition" than a complete change of genetic
substrate.

Maybe this sort of thing will change as the modern genetic takeover gathers steam.
--
__________
|im |yler http://timtyler.org/ [email protected] Remove lock to reply.
 
Jim Menegay wrote:

>
> I disagree that Cairns-Smith's work has been neglected. His idea of genetic takeover, and his
> metaphor of the arch are enormously influential. Same goes for his pointing out the relevance of
> surface chemistry to people who only understand solution chemistry.
>
> Yes, the specific idea of clay is out of favor now, and, personally I believe that there are good
> reasons for this, but even if pyrite replaces clay as the magic mineral of choice, historians will
> still point to Cairns-Smith's ideas as pivotal.
>
As far as I know, pyrites are not envisaged as carriers of genetic information in the way that Cairns-
Smith envisages for clay. This key concept embodied in Cairns-Smith's theory seems to me to be very
largely disregarded.

> Tyler expects too much of a sluggish establishment. How many years did it take before Oparin's
> ideas became mainsteam?

Interesting. I don't think one could say that Oparin's ideas are mainstream today. In spite of the
problems of resolving Eigen's paradox (ie how, without highly evolved replication mechanisms,
template molecules managed to replicate accurately enough to get the process of evolution going),
and the difficulty of explaining the origin of chiral molecules, the mainstream today seems to be
very much based around the RNA world theory and its successors.

I suppose that the Oparin Haldane metabolic view of the origin of life may have been influential in
the West during the late forties and early fifties, during the time leading up to the Miller-Urey
experiment. On the other hand, Erwin Schrödinger's 1945 book "What is Life?" with its idea of an
"aperiodic crystal" represents an unequivocally genetic view of the origin.

Oparin's first book was published in 1924, but according to Wills and Bada in 'The Spark of Life'
seems that he had considerable difficulty getting it published. They write "Only later was he
[Oparin] embraced by the communist regime".

Since the Fifities and the discovery of Watson and Crick (and Franklin and Wilkins!), it seems to me
that the mainstream view has been very much the idea that the key mechanism in the origin of life
was a carbon based template replicating molecule (eg DNA / RNA). The Oparin - Haldane idea of a
metabolic origin has been very far from mainstream.

The ideas of Oparin and Haldane are however not completely ignored today in the way that Cairns-
Smith's seem to be. I do think that it is valid at least to ask what the major objections are to
the theory.

--
Chris Gordon-Smith London Homepage: http://graffiti.virgin.net/c.gordon-smith/ Email Address: Please
see my Home Page
 
TomHendricks474 <[email protected]> wrote or quoted:
> << Here's my take on the matter:

> 1. Can you outline a complete scenario from clay to the point where there is metabolism,
> replcation, and a dividing cell - maybe even an RNA world.

Goodness, no!

Possible bits of this story have been told. My only contribution so far has been the (somewhat
speculative :>) material on:

http://originoflife.net/sweet_crystal/

...which offers a clay-polysaccharide bridge scenario.

For most of the rest of the story, I have to refer you to Cairns-Smith's writings:
http://originoflife.net/cairns_smith/

However, I can give a very brief statement on the matter:

The important thing is the origin of an evolving, self-reproducting system.

Once that is in place the rest of the story can be explained as the result of technology developed
by the early organisms in the process of adapting to their environment.

The details are of historical interest - but as long as there is *some* possible path, we can wave
our hands a bit and say "life found a way".

> 2. What environmental conditions is all this happening in? And how does the daily sun heat cycle,
> and the seasonal change on earth effect this scenario?

Some liquid water on the edge of supersaturation somewhere.

The primitive oceans bottom would be a suitable location.

Super-saturated solutions are made all over the planet by the action of rain on rock surfaces. Sun
energy forms rain, which dissolves rock which runs into rivers that reaches the ocean and then
crystallises.

Any excess material rapidly crystallises out - leaving bodies of water "on the edge" of super-
saturation - balanced at the point where crystal formation is most reliable - and crystals neither
dissolve too quickly - or form too rapidly to correct defaults during construction.

The primitive earth - and the earth today - is a gigantic clay-making machine.
--
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Anthony Cerrato <[email protected]> wrote in message news:<[email protected]>...
> ...[Snip]... The only question is where do genes come from?--Are there any good models outside of
> Kaufman-like autocatylytic enzyme chains in a non-linear dynamic "soup" far from
> equilibrium...chaos...and chance? ...tonyC

If you have something that can exist in different variants, and can reproduce itself when the
"owning" organism reproduces, then you have a gene. But notice that the variation must itself be
reproducible.

There are also some stability requirements - the gene should usually not change to a different
variant over the life cycle of the organism. If you want your gene to be part of a large genome,
then Eigen suggests that the mutation rate has to be fairly low.

Given these requirements, I know of four different kinds of models for genes:

1. Linear polymers - for example nucleic acids.
2. Crystals with a sheet structure - for example clay.
3. Ecosystems.
4. Attractors in dynamical systems.

The ecosystem idea requires that the organism that you want to have "own" the genes is, in some
sense, an ecosystem of smaller organisms. These smaller organisms must reproduce, but they don't
need to have their own genetics - we are dealing here with small "organisms" that cannot themselves
evolve. However, the ecosystem can evolve. The ecosystem has one gene-locus for each small
"species". The two possible alleles for each locus are "It exists" and "It doesn't". Your ecosystem
can have mutation due to extinctions and spontaneous generations of its constituent species. There
is also the possibility of horizontal gene transfer. The main difficulty is in coming up with
ecosystems that reproduce in a way that carries ALL of the parent ecosystem's species into the child
ecosystem.

The attractor idea is even more abstract. The system state tends to migrate toward one or another
"attractor" in the state space. And, without some perturbation, it will stay there. Change the
environment slightly, and the exact coordinates of the attractor change too, but it is still, in
some sense, the same attractor. But give the environment a temporary jolt, and the system may
jump to the "basin of attraction" of a different attractor. So you get a mutation. The main
difficulty with this attractive proposal is that to have many genes, you need many independent
dynamical systems all running within the same organism. You also need a mode of reproduction that
partitions the dynamic state space into two organisms without seriously disturbing the dynamic
state. That is a problem for any attempt to make genes out of the dynamics of membranes. There
are attractors in these dynamics, to be sure, but fission is likely to disrupt that dynamics. The
dynamics of cytosolic chemistry, by contrast, is easily reproduced by simply partitioning the
cytosol into two parts.

I am not aware of any realistic examples of these last two kinds of gene models.

If anyone knows of any other kinds of models, I would also like to hear about them.
 
Anthony Cerrato <[email protected]> wrote in message news:<[email protected]>...
> ... [Snip] ...The only question is where do genes come from?--Are there any good models outside of
> Kaufman-like autocatylytic enzyme chains in a non-linear dynamic "soup" far from
> equilibrium...chaos...and chance? ...tonyC

It is odd, to say the least, to respond twice to the same question, especially when the question was
not directed to me. ;-/ But it occurs to me, on reflection, that my first answer may have completely
missed your point.

Are you suggesting that some other process (besides natural selection) is needed in order to somehow
"bootstrap" a collection of random genes into a collection of somewhat effective genes? And, that
natural selection cannot, somehow, "gain traction" until this takes place? That only a somewhat-
effective starter system can evolve to a very-effective final system under natural selection?

I suspect that Tim would deny that any such bootstrap process is needed. Me, I'm intrigued by the
suggestion, but dubious that Kauffman is on the right track regarding the nature of the bootstrap,
if one is actually needed.
 
Chris Gordon-Smith <[email protected]> wrote or quoted:

> I suppose that the Oparin Haldane metabolic view of the origin of life may have been influential
> in the West during the late forties and early fifties, during the time leading up to the Miller-
> Urey experiment. On the other hand, Erwin Schrödinger's 1945 book "What is Life?" with its idea of
> an "aperiodic crystal" represents an unequivocally genetic view of the origin.

It appears that J.B.S. Haldane ought to go into the "naked gene" camp - with Cairns-Smith - e.g.:

``J.B.S. Haldane and A.I. Oparin, despite being co-progenitors of this biogenesis paradigm,
disagreed on the specific order of events in the origin of life. Oparin postulated that cells were
created first, then enzymes, and then genes last. [...]

Haldane, on the other hand, believed that genes came first, then enzymes, and lastly came cells.
Leslie E. Orgel and Manfred Eigen explain the sequence as follows: self-replicating RNA would be
followed shortly by enzymes that with the RNA produced a primitive transcription system, that
would eventually be enclosed by a cell for “physical cohesion.” Genes also seem structurally
simpler than enzymes. With Crick and Watson’s elucidation of the structure of DNA it became
“…natural to think of the nucleic acids as primary and of the proteins as secondary…. This
sequence of events that places genes first can be thought of as the “naked gene” position.''

- http://www.stanford.edu/group/STS/techne/Fall2002/srinivasan1.htm
--
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Jim Menegay <[email protected]> wrote or quoted:

> I know of four different kinds of models for genes:
>
> 1. Linear polymers - for example nucleic acids.
> 2. Crystals with a sheet structure - for example clay.

I would sub-divide Crystals into:

* 1D genes;
* 2D genes;
* 3D genes;

1D and 2D crystal genes are as described on:

http://originoflife.net/information/

3D genes are described on:

http://originoflife.net/3d_genes/

3D genes are unlikely to be plausable as early genes. However they are possible in theory.

It was once argued that:

``On the other hand the information itself must not be three-dimensional if it is to be at all
easily replicated; for a simple copying process there should be at least one spare dimension for it
to be replicated into.'' - Seven Clues to the Origin of Life [1] p. 95.

...but it turns out that this isn't necessary - 3D genes /could/ still be replicated under primitive
conditions - *despite* their space-filling properties - through the use of a screw dislocation.

"3D" might be seen as a bit of a misnomer - since it might be better to ascribe some fractal
dimension between 2 and 3 to these sorts of genes.

> 3. Ecosystems.
> 4. Attractors in dynamical systems.

> I am not aware of any realistic examples of these last two kinds of gene models.

Yes - that about describes the situation - IMO.
--
__________
|im |yler http://timtyler.org/ [email protected] Remove lock to reply.
 
Jim Menegay <[email protected]> wrote or quoted:
> Anthony Cerrato <[email protected]> wrote:

>> The only question is where do genes come from?--Are there any good models outside of Kaufman-like
>> autocatylytic enzyme chains in a non-linear dynamic "soup" far from equilibrium...chaos...and
>> chance?

[...]

> Are you suggesting that some other process (besides natural selection) is needed in order to
> somehow "bootstrap" a collection of random genes into a collection of somewhat effective genes?
> And, that natural selection cannot, somehow, "gain traction" until this takes place? That only a
> somewhat-effective starter system can evolve to a very-effective final system under natural
> selection?
>
> I suspect that Tim would deny that any such bootstrap process is needed. Me, I'm intrigued by the
> suggestion, but dubious that Kauffman is on the right track regarding the nature of the bootstrap,
> if one is actually needed.

I usually take "genes" to refer to the heritable bits of a model - rather than to some specific
physical entity - so "before genes" there can have been no natural selection going on.

What /did/ exist before evoultion started was ordinary physics and chemistry. There is substantial
scope for these exhibiting complex phenomena - from processes usually described using the term "self-
organisation".

Plainly my preferred explanation invokes such self-organisation, prior to the origin of self-
reproduction.

Crystal growth is a classic example of highly ordered structures forming out of a disordered
molecular soup.
--
__________
|im |yler http://timtyler.org/ [email protected] Remove lock to reply.
 
Chris Gordon-Smith <[email protected]> wrote in message news:<[email protected]>...

> The ideas of Oparin and Haldane are however not completely ignored today in the way that Cairns-
> Smith's seem to be. I do think that it is valid at least to ask what the major objections are to
> the theory.

Well, I had been hoping that at least one of Orgel, Pace, Maynard-Smith, Eigen, deDuve, Fox, Miller,
or Dyson would respond to your challenge. Since they have chosen not to, I'll give it a try.

Here are 9 anti-clues. ;-)

1. Spontaneous Generation - Paradoxically, clay naked genes are TOO easy to create. In order for
natural selection to make "progress", spontaneous generation must be rare. The vast majority of
production must be re-production, otherwise the progress made by selection is diluted by newly
created random genes. The clay theory can overcome this, perhaps, but only at a cost. After all,
any environment that gives you the free growth that you want may also give you spontaneous
generation that you don't want. The clay theory loses credibility because it doesn't appear to
face this difficulty squarely.

2. Naked and Boring - It is far from clear that a naked gene can evolve into anything interesting
unless there is a simple path from naked genes to a naked genome. For RNA, this is easy - join
the genes together end to end. The corresponding process for clay is less obvious. Experimental
work that has been done on the test-tube evolution of naked genes in RNA and Artificial-Life seem
to indicate that natural r-selection leads to the gene becoming simpler and simpler. Only if the
experimenter supplies some kind of artificial selection does anything interesting happen in terms
of phenotype.

3. Genetic Takeover Motivation - The notion of genetic takeover is central to the clay theory, and
it seems plausible both in terms of bio-physics and natural selection. Plausible, but not
required. I would like to see a theoretical analysis of a system with two genetic materials that
suggests reasons why and how one of those materials would eventually supplant the other. Without
such a theory, I have to rely on my intuition, which suggests to me that neither material would
completely disappear. There is also some question as to why the second material would even arise.
Looking at the history of life since the RNA world, we see the genetic material being used to
supply new kinds of meanings, some very indirectly, but no cases in which new genetic materials
are tried, as far as I know.

4. Metabolism - Something more cogent than the handwaving I have seen so far is needed to convince
me that naked clay genes would be able to create even the beginnings of the wonderful and
wonderfully complicated system of organic reactions that provide autopoeisis and reproduction to
life as we know it today. At the very least, clay has to create the material and energetic basis
of the successor genetic system, as well as the organismic "glue" or container that permits both
genetic systems to exist within a single neo-Darwinist organism. If clay cannot do this, then I
think that it would be a mistake to say that clay is _ancestral_ to modern life.

5. Heterotrophy - Personally, I find it implausible that random organic molecules generated by pre-
biotic chemistry could have any part in the origin of a modern bio-chemistry that is remarkably
non-random and stereospecific. But the clay theory seems to require that the first interactions
between clays and organics involved random organics. I would be much more impressed if you made
the organics yourself, making use of the the stereospecificity of your own genetics to produce
non-random chiral organic helper molecules from achiral C1 units.

6. Organismic Takeover - As sketched elsewhere, I am impressed by the fact that modern cells are
surrounded by membranes, and I want a clear explanation of how this came about. Diagrams like
those of JMS&ES look to me as if they describe an ontogenic progression, rather than the needed
philogenic progression. When I try to use recapitulation ideas to show both progressions, I am
unable to come up with a scheme which avoids a "saltation" in the philogeny. This issue seems
most severe for ideas like clay which require non-lipid-soluble nutrients for growth. The problem
disappears if the crystals and thus the genetics live on the OUTSIDE surface of the liposome. I
would be more impressed with the clay theory if it took this idea and ran with it, rather than
simply ignoring membranes and cellular morphology as unimportant details.

7. Error Catastrophe - Clay has to face this problem, just as RNA does. I don't suggest that the
problem has been ignored, but it is far from clear to me that it has been solved. Part of the
problem is that Eigen's arithmetic of mutation rates is familiar arithmetic. Mutation of the
flaws in a crystal structure is a more difficult concept for me to try to develop a quantitative
feel for. So this objection may simply be that I have been too lazy to invest the necessary study
into crystal structure. But, I notice that Tyler's references page quotes Wills and Bada as
saying bluntly "Unfortunately for his idea, it quickly became apparent that minerals simply could
not carry enough information to be the genetic material for even the most primitive life." And,
when you look at Cairns-Smith's publication history, it seems that he himself moved away from
clay genetics to a weaker stance that clays might have been important as one pre-biotic catalyst.

8. Separation of Genotype and Phenotype. RNA has the virtue that it exists in two forms. There is a
double-stranded form that stays home and replicates. And there is a sterile single-strand form
that goes out into the world and gets its hands dirty doing "real work". Since the genomic form
does not do "real work", it avoids being damaged by use. It is not clear to me how clay could
achieve this. (Though perhaps a scheme like the macro-nucleus/micro-nucleus of some protozoa...)

9. Phenotype Wimpiness. This one may be based on ignorance, rather than knowlege... Although it is
rarely stressed, "roller-coaster" graphs showing free energy against a reaction coordinate
involve the presence of real Newtonian forces within the substrate. Newton's third law requires
that there be opposite forces within the enzyme. You need to catalyse strong covalent bonds, but
your "enzyme" is constructed using weak electrostatic bonds. (I know this argument is enormously
oversimplified, but it contains a kernel of truth.) Therefore your clay crystal, which is also
your genome, will tear itself apart if it attempts to do any really heavy lifting. I realize that
clays are used as industrial catalysts, which sounds impressive. But I don't know whether those
clay catalysts draw their efficacy from the periodic or the weaker aperiodic features of the
crystal. I also don't know how rapidly these catalysts become "poisoned" in their industrial
applications. There are people using artificial selection to generate protein enzymes and
ribozymes for industrial use. Has anything like this been done for clay?

Those are the objections I have. But, then, I am not a member of the establishment.

It occurs to me that one reason the establishment ignores the clay theory is that the clay theory
ignores the establishment. It does not even address the problems that most other OOL researchers are
working on. It seems to consist of one cute idea, plus a lot of hand-waving that claims to show that
those other problems are irrelevant. That kind of challenge is easy to ignore, especially when you
have invested much of your professional life on solving that problem.
 
Tim Tyler wrote:

> Chris Gordon-Smith <[email protected]> wrote or quoted:
>
>> I suppose that the Oparin Haldane metabolic view of the origin of life may have been influential
>> in the West during the late forties and early fifties, during the time leading up to the Miller-
>> Urey experiment. On the other hand, Erwin Schrödinger's 1945 book "What is Life?" with its idea
>> of an "aperiodic crystal" represents an unequivocally genetic view of the origin.
>
> It appears that J.B.S. Haldane ought to go into the "naked gene" camp - with Cairns-Smith - e.g.:
>
> ``J.B.S. Haldane and A.I. Oparin, despite being co-progenitors of this biogenesis paradigm,
> disagreed on the specific order of events in the origin of life. Oparin postulated that cells were
> created first, then enzymes, and then genes last. [...]
>
> Haldane, on the other hand, believed that genes came first, then enzymes, and lastly came cells.
> Leslie E. Orgel and Manfred Eigen explain the sequence as follows: self-replicating RNA would be
> followed shortly by enzymes that with the RNA produced a primitive transcription system, that
> would eventually be enclosed by a cell for “physical cohesion.” Genes also seem structurally
> simpler than enzymes. With Crick and Watson’s elucidation of the structure of DNA it became
> “…natural to think of the nucleic acids as primary and of the proteins as secondary…. This
> sequence of events that places genes first can be thought of as the “naked gene” position.''
>
> - http://www.stanford.edu/group/STS/techne/Fall2002/srinivasan1.htm

Thanks for this useful link. I suppose that the Oparin-Haldane hypothesis should be regarded as the
idea of the prebiotic soup, rather than specifically the 'metabolism first' idea.
--
Chris Gordon-Smith London Homepage: http://graffiti.virgin.net/c.gordon-smith/ Email Address: Please
see my Home Page
 
Tim Tyler <[email protected]> wrote in message news:<[email protected]>...
> ``J.B.S. Haldane and A.I. Oparin, despite being co-progenitors of this biogenesis paradigm,
> disagreed on the specific order of events in the origin of life. Oparin postulated that cells were
> created first, then enzymes, and then genes last. [...]
>
> Haldane, on the other hand, believed that genes came first, then enzymes, and lastly came cells.

Logically, before neo-Darwinism kicks in, you need all three.

Cells (or more generally "containers") are ORGANISMS Genes (or more generally "information") are
GENOTYPE Enzymes (or more generally "denotations") are PHENOTYPE

Clay is exciting because it can give you GENOTYPE easier than any other approach.

RNA is exciting because it gives you both GENOTYPE (when double stranded) and PHENOTYPE (when single
stranded).

Lipids excite a few people. They yield ORGANISMS, of course. But many people are very unexcited.
Naked genes could also suffice as organisms.

We (think we) know of at least one case of "phenetic takeover". Enzymes replaced ribozymes.

We can easily imagine "genetic takeovers".

But only a few people worry that "organismic takeovers" might be more difficult to pull off. How do
you gradually evolve a membrane? If you find yourself inside one by accident, how do you maintain
your old life-style?
 
Thanks for your comments. I interleave my replies:

Jim Menegay <[email protected]> wrote:

> 1. Spontaneous Generation - Paradoxically, clay naked genes are TOO easy to create. In order for
> natural selection to make "progress", spontaneous generation must be rare. The vast majority of
> production must be re-production, otherwise the progress made by selection is diluted by newly
> created random genes.

This is inaccurate. There is no good reason at all for spontaneous generation being rare. Newly
created random genes are only a threat to existing organisms if they are effective at competing with
them for resources - and there is no compelling reason why this should be so.

I expect spontaneous generation is going on all the time today - it's just that the organisms so
created never have a hope of getting very far in the face of sophisticated, high- tech competion
from today's more highly-developed organisms
- which eat their lunch.

> 2. Naked and Boring - It is far from clear that a naked gene can evolve into anything interesting
> unless there is a simple path from naked genes to a naked genome. [...]

Clay organisms would have genotpyes consisting of many bits of information.

They would have always been "naked genes" rather than a "naked gene".

I consider it part of the definition of living organisms that they have more than a "trivial" level
of heritable information - and so I would not regard anything with only a few bits of heritable
information as alive in the first place.

Clays certainly have substantial information-carrying capacity - in terms of fault structures.

> For RNA, this is easy - join the genes together end to end. The corresponding process for clay is
> less obvious.

? I don't know what you mean. The corresponding process for clay seems to be /exactly/ as obvious -
since it is /exactly/ the same - at least for 1D clay genes. Like RNA, clay forms "aperiodic
crystals", using a template-copying mechanism.

The (more-likely-IMO) 2D clay genes don't suffer from this problem either - rather than stringing
genes together on a thread they are laid down next to one another on a 2D lattice.

I can see no coherent objection along the lines that there are problems compositing genes together
in clay organisms. If there is anything here, please spell out the objection more clearly.

> Experimental work that has been done on the test-tube evolution of naked genes in RNA and Artificial-
> Life seem to indicate that natural r-selection leads to the gene becoming simpler and simpler.

That's true - though this is an objection equally applicable to any origins scenario.

> Only if the experimenter supplies some kind of artificial selection does anything interesting
> happen in terms of phenotype.

This isn't a "clay-specific" objection.

What probably happened in the case of clays was that there was selection for large size. Large
crystals can have some advantages over small ones in some environments - in particular, they are
less likely to spontaneously dissolve during local fluctuations in the level of saturation.

I suspect that the key selector for large size was gravity. Large crystals have different phenotypic
properties in gravitational fields - due to their large mass and relatively small surface area. They
are less susceptable to perturbations from thermal motion, and might well win any downhill races in
streams - thus colonising new regions downstream first.

> 3. Genetic Takeover Motivation - The notion of genetic takeover is central to the clay theory, and
> it seems plausible both in terms of bio-physics and natural selection. Plausible, but not
> required. I would like to see a theoretical analysis of a system with two genetic materials
> that suggests reasons why and how one of those materials would eventually supplant the other.
> Without such a theory, I have to rely on my intuition, which suggests to me that neither
> material would completely disappear.

The clay theory *does* suggest the *original* genetic material will disappear.

> There is also some question as to why the second material would even arise.

Originally, for structural reasons - long chain organic polymers have utility as scaffolding. There
are some other possibilities as well - but scaffolding seems one of the most likely reasons.

> Looking at the history of life since the RNA world, we see the genetic material being used to
> supply new kinds of meanings, some very indirectly, but no cases in which new genetic materials
> are tried, as far as I know.

The modern world is full of new information-carrying media, which are used by organisms to transmit
heritable information to their offspring.

Indeed a modern genetic takeover seem inevitable.

See http://originoflife.net/takeover/

...for more details.

If you think about the modern situation, it should be abundantly clear how and why new information-
carrying media can come onto the scene.

> 4. Metabolism - Something more cogent than the handwaving I have seen so far is needed to convince
> me that naked clay genes would be able to create even the beginnings of the wonderful and
> wonderfully complicated system of organic reactions that provide autopoeisis and reproduction
> to life as we know it today. At the very least, clay has to create the material and energetic
> basis of the successor genetic system, as well as the organismic "glue" or container that
> permits both genetic systems to exist within a single neo-Darwinist organism. If clay cannot do
> this, then I think that it would be a mistake to say that clay is _ancestral_ to modern life.

This all seems irrelevant to me. Modern life *did* form. Either it happened by chance, or some
earlier organisms constructed it.

Earlier organisms stand a hugely greater chance of creating more complex lifeforms than chance does
- since they can use evolution via natural selection to do assist them. Consequently it makes good
sense to continue to invoking construction by "earlier organisms", until the "earlier organisms"
have a fair chance of appearing from nothing - rather than dabbling with the fantastic odds of more
complex creatures self-assembling themselves.

Constructing plausible "just so" stories is certainly interesting and fun - and there have been a
number of attempts to fill in parts of the story. However these events happened a long time ago, and
left few clues about the actual details.

It doesn't seem terribly important as an objection to the theory which path actually happened.

The only thing I would consider as a valid objection is the assertion that it is possible that no
such path from primitive clay based organisms to modern life forms exists - or that organic life had
more chance of being constructed by chance than it did of being built during the struggles between
the clay organisms.

I think this latter notion is ridiculous. It boils down to claiming that random processes have a
better chance of building some complex structure than existing organisms in an ecosystem do.

My money goes firmly on the existing organisms in this instance. The grooves on the surfaces of clay
minerals are excellent catalysts of organic reactions. They would have had both the means and the
motivation to dabble in organic chemistry.

> 5. Heterotrophy - Personally, I find it implausible that random organic molecules generated by pre-
> biotic chemistry could have any part in the origin of a modern bio-chemistry that is remarkably
> non-random and stereospecific. But the clay theory seems to require that the first interactions
> between clays and organics involved random organics. I would be much more impressed if you made
> the organics yourself, making use of the the stereospecificity of your own genetics to produce
> non-random chiral organic helper molecules from achiral C1 units.

"Natural" clay chirality from things like screw dislocations might conceivably help is resolving
problems with selectively building chiral components.

As far as "making organic compounds themselves" goes, clay mineral organisms would have had to work
with whatever was in their immediate environment.

Whatever the source of the first organic compounds, they are bound to be *much* easier to synthesize
if there are some existing organisms around, engaged in competition with one another - and
deliberately making organic compounds to affect things like the stickiness of their immediate
environment - and inhibiting "lateral" crystal growth.

The alternative is that inorganic processes performed the feat. Evaporation from rock pools purified
the chemicals - and so on.

> 6. Organismic Takeover - As sketched elsewhere, I am impressed by the fact that modern cells are
> surrounded by membranes, and I want a clear explanation of how this came about.

...but the details don't much matter for the origin of life. However it happened, it will happen a
hell-of-a-lot easier if there are existing organisms around fighining one another for control of the
local organic chemicals in the environment.

Sure the origin of cells is interesting - but it happened well after the origin of life. As far as
that puzzle goes, the origin of cells is a bit of an irrelevant distraction.

> Diagrams like those of JMS&ES look to me as if they describe an ontogenic progression, rather than
> the needed philogenic progression. When I try to use recapitulation ideas to show both
> progressions, I am unable to come up with a scheme which avoids a "saltation" in the philogeny.
> This issue seems most severe for ideas like clay which require non-lipid-soluble nutrients for
> growth. The problem disappears if the crystals and thus the genetics live on the OUTSIDE surface
> of the liposome. I would be more impressed with the clay theory if it took this idea and ran with
> it, rather than simply ignoring membranes and cellular morphology as unimportant details.

You are trying to make a complex point here - and I have some sympathies with the point you are
trying to make.

Clay minerals were (IMO) never inside a membrane. As you suggest, membranes and clay don't mix. Nor
were they ever attached to the outside of it.

What I *suspect* happened was that the clay "naked genes" gave rise to a complex ecosystem that was
then able to support organic "naked" replicators as a small element of that ecosystem.

I was these organic genes (or their distant descendants) that took up residence beneath blisters of
lipid material on mineral surfaces - and eventually became the first cells.

Other scenarios are possible - but this is an example of a plausible possibility.

> 7. Error Catastrophe - Clay has to face this problem, just as RNA does. I don't suggest that the
> problem has been ignored, but it is far from clear to me that it has been solved. Part of the
> problem is that Eigen's arithmetic of mutation rates is familiar arithmetic. Mutation of the
> flaws in a crystal structure is a more difficult concept for me to try to develop a
> quantitative feel for. So this objection may simply be that I have been too lazy to invest the
> necessary study into crystal structure. But, I notice that Tyler's references page quotes Wills
> and Bada as saying bluntly "Unfortunately for his idea, it quickly became apparent that
> minerals simply could not carry enough information to be the genetic material for even the most
> primitive life."

Wills and Bada did not show much sign of knowing much about the clay theory - and yet were put in
the position of having to present *some* reason for rejecting it.

IMO, the objection they picked is a ridiculuos one. Clays may have problems - but information
capacity is not one of them.

Demonstrating that your genes can avoid an error catastrophe is a problem for all OOL theories.

Clay seems better placed that most - since there is a built-in error correction device in the
process of crystal formation - any clays naturally form highly regular crystalline structures, under
plausible prebiotic conditions.

No mixture of organic chemicals produces anything like the highly organised regular patterns seen
in crystals.

Plausible prebiotic organic chemicals self-organise to form approximately one structure - besides
the tangled mess - and that's the sphere. Unfortunately, spheres are practically useless as the
basis of a system of heritable information transfer, and lack any sign of a template-copying
mechanism.

The key to primitive genetic systems is crystals and their associated natural template-copying
system, and - as a rule of thumb - organic chemicals are absolutely rubbish at forming crystals ;-)

> And, when you look at Cairns-Smith's publication history, it seems that he himself moved away from
> clay genetics to a weaker stance that clays might have been important as one pre-biotic catalyst.

That appears inaccurate to me.

Cairns-Smith sent me his 2001 paper on the subject. It includes many pages describing and
elucidating his theory of clay genetics - including modern material which was previously unfamiliar
to me relating to his study of long distance repeating structures in barium ferrites.

However, it should be said that some element of focus of clays as organic catalysts seems
practically inevitable in the field - since that sort of research is what gets funded by the
industries which are interested in such reactions.

Many people want to find effective organic catalysts - while relatively few are interested in the
origin of life.

> 8. Separation of Genotype and Phenotype. RNA has the virtue that it exists in two forms. There is
> a double-stranded form that stays home and replicates. And there is a sterile single-strand
> form that goes out into the world and gets its hands dirty doing "real work". Since the genomic
> form does not do "real work", it avoids being damaged by use. It is not clear to me how clay
> could achieve this. (Though perhaps a scheme like the macro-nucleus/micro-nucleus of some
> protozoa...)

Clay genes have a phenotype much like any other sort of gene does.

It is difficult to imagine an information storage device where the information on it does *not*
affect its copying frequency.

The most obvious aspects of the phenotype of clay genes consists of things like their weight, and
the pattern of domains that gets replicated during crystal growth - which affects stability,
breaking strength.

In a more sophisticated scenario, the (replicated) cross section of a 2D clay gene produces a
pattern of grooves on the surface of the resulting crystal. Different patterns of grooves may
catalyse different reactions between organic chemicals also present in solution. Similarly
groove patterns (and their associated gunk) may affect the ability of the crystals to roll, move
past one another, or stick together - all significant aspects of your phenotype - if you are a
crystal organism.

> 9. Phenotype Wimpiness. This one may be based on ignorance, rather than knowlege... Although it is
> rarely stressed, "roller-coaster" graphs showing free energy against a reaction coordinate
> involve the presence of real Newtonian forces within the substrate. Newton's third law requires
> that there be opposite forces within the enzyme. You need to catalyse strong covalent bonds,
> but your "enzyme" is constructed using weak electrostatic bonds. (I know this argument is
> enormously oversimplified, but it contains a kernel of truth.) Therefore your clay crystal,
> which is also your genome, will tear itself apart if it attempts to do any really heavy
> lifting.

Perhaps there's some truth to this. I think in practice, the bigger effect will be that the clay
"needles" will break under their own weight - an effect that will actually help them to reproduce.

Clays might be genetic (and phenotypic) wimps in a sense - but they only need to cause enough
selection to prevent error catastrophes in their own small genomes.

> I realize that clays are used as industrial catalysts, which sounds impressive. But I don't know
> whether those clay catalysts draw their efficacy from the periodic or the weaker aperiodic
> features of the crystal.

The *main* effect tends to involve grabbing organic molecules out of solution and holding them right
next to one another for a period of time.

> There are people using artificial selection to generate protein enzymes and ribozymes for
> industrial use. Has anything like this been done for clay?

Not that I know of - though of course Cairns-Smith proposed doing this, e.g. on the last page of
"Genetic Takeover".

The biggest problem is that we have no good replicating clay organisms to work from - so we are
forced to use natural clays - which tend to be more higgle-de-piggledy and random.

> It occurs to me that one reason the establishment ignores the clay theory is that the clay theory
> ignores the establishment. It does not even address the problems that most other OOL researchers
> are working on.

Most of the problems other OOL researchers address are not *actually* very relevant to the origin of
life. They relate to things like the origin of cells - which came later.

Whatever the solution to those problems is, it is *bound* to happen much more easily if evolution
via natural selection is permitted to be mentioned in the explanation - i.e. if there are existing
organisms around to invent the technology that solves the problem.

> It seems to consist of one cute idea, plus a lot of hand- waving that claims to show that those
> other problems are irrelevant. That kind of challenge is easy to ignore, especially when you have
> invested much of your professional life on solving that problem.

Cairns-Smith's idea probably pisses off the people who have devoted their lives to theorising how
nutrients can possibly have got into and out of prebiotically-plausible cell membranes - since it
says that such work won't throw much light on life's origin - since it post-dated the event.

I can't do much about that - if you do want to study stuff that's relevant to life's *actual*
origin, it's up to you to expend your energy in the correct location.
--
__________
|im |yler http://timtyler.org/ [email protected]
 
Jim Menegay <[email protected]> wrote or quoted:
> Tim Tyler <[email protected]> wrote in message news:<[email protected]>...

> Logically, before neo-Darwinism kicks in, you need all three.
>
> Cells (or more generally "containers") are ORGANISMS Genes (or more generally "information") are
> GENOTYPE Enzymes (or more generally "denotations") are PHENOTYPE

You don't need a "container" to get an evolving system - since there is another way for organisms to
maintain their integrity in the face of environmental perturbations - besides putting all their bits
in a box - namely, gluing themselves together.

That's the essence of the "naked gene" approach.

> Clay is exciting because it can give you GENOTYPE easier than any other approach.
>
> RNA is exciting because it gives you both GENOTYPE (when double stranded) and PHENOTYPE (when
> single stranded).

You can't really *avoid* having a phenotype. If information is being copied it's practically bound
to influence its own copying frequency to *some* extent.

Clays have their own abilities in this area. In particular their (inherited) cross section creates a
pattern of grooves on their outer surface. These grooves trap organic molecules from their
environment - and then these in turn stick to one another - and to nearby objects - and can have a
big effect on the stickiness and viscosity of the clay - which affect its ability to avoid getting
washed away - or to spread to new locations.

> We can easily imagine "genetic takeovers".
>
> But only a few people worry that "organismic takeovers" might be more difficult to pull off. How
> do you gradually evolve a membrane? [...]

Barriers that hold things together can be built on many scales - from cell walls to sea shells and
insect exoskeletons - so they have evolved on multiple occasions.

The original evolution of cell membranes is hypothesised to have ocurred on mineral surfaces -
with a lipid layer initially binding loosely to the surface, and then forming blisters and
eventually cells.

The gap between the mineral surface and the lipid layer provides nutrients and exhaust routes -
since expecting very much to make it through a primitive membrane is not very resonable.

See, "The Origins of Life" - JMS & ES, p. 56 for a diagram.
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|im |yler http://timtyler.org/ [email protected] Remove lock to reply.
 
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